Helicobacter pylori chronically infect the human stomach of half the world and approximately a third of the US population. H. pylori induces inflammation in all hosts and 10-20% of those infected will present with severe disease including peptic ulcers and gastric cancers. All H. pylori associated diseases depend on the ability of this organism to establish a persistent infection and induce chronic inflammation. Thus H. pylori disease is a by-product of the interaction between bacterial factors necessary for establishing and maintaining infection and the resultant host defenses. This interaction is dynamic with both the bacteria and host changing over decades of infection. To study this complex process, we utilize a mouse model of infection and we study genetic variation among isolates from human clinical populations. Work in previous funding periods established tools and methods necessary to take a functional genomic approach to define molecular mechanisms of pathogenesis for this organism, which is evolutionary distant from better studied enteric pathogens, including whole genome sequencing, in vivo colonization screens, and both random and an ordered sequence defined mutant libraries. Convergence of our genetic and population-based studies drives the focus of our proposed studies on DNA repair, uptake and genetic diversification as well as cell envelope proteins that appear to influence host responses. This will be accomplished in three Aims that: 1. Evaluate DNA repair as a target for H. pylori eradication therapy, 2. Explore the mechanisms and consequences of genetic variation during transmission and chronic infection, both in humans and a mouse stomach colonization model, and 3. Perform functional analysis of bacterial factors that promote and inhibit infection. Our study of the genes contributing to virulence will identify the mediators of persistent infection and studies of genetic variation in te clinical population will show how these mediators adapt during the chronic inflammation that is associated with infection and leads to severe disease (ulcer, cancer). Our study of the mechanisms by which H. pylori promotes genetic exchange and diversification should also increase understanding of the spread of antimicrobial resistance, an increasing clinical problem in the treatment of H. pylori, thus advancing the mission of NIAID to understand and treat infectious diseases.